Linkage disequilibrium in two-stage marker-assisted selection

The advantage of using marker-assisted selection (MAS) to pre-select betwee n animals of identical pedigree prior to progeny testing was investigated f or a single generation In particular, the dis-equilibrium induced by MAS am ong full sibs was compared with that of traditional pedigree selection with out knowledge of Mendelian segregation. Stochastic simulation was used to m odel a situation similar to dairy cattle improvement schemes to generate a large base population from which dams and Fires were selected on a single s ex-limited index trait. The trait was meddled with a polygenic component, a non-genetic component and two additive, diallelic and physically unlinked loci of major effect. A two stage selection was applied on the offspring. T n the first stage, QTL (Quantitative Trait Loci) information was used to se lect within each full-sib family from highly selected parents. Alternativel y, selection was at random within elite families. In the second stage,selec ted males were progeny tested performance used for selection. Total genetic response and QTL response were always higher with MAS. With QTL of moderat e size and starting frequencies of 0, 1 for the favourable alleles, the adv antage of MAS over traditional schemes was 5.3 % for rural genetic response and 32.9 % for QTL response. The polygenic response was very similar for b oth selection schemes, At low initial frequencies of favourable alleles, th e traditional scheme showed slightly less depression of polygenic response than MBS while the opposite was true for higher starring frequencies. Diseq uilibrium values between polygenes and QTL and between the two QTL. were al ways negative in both schemes. Marker-assisted selection often resulted in less negative disequilibrium between polygenes and QTL than traditional sel ection.